Data Intake

Indexstubfiledata_typetaxon_stringtranslation_table
0KX808498-truncatedKX808498-truncated.gbGenBankCaulerpa_cliftonii_HV0379811
1KY509313-truncatedKY509313-truncated.gbGenBankAvrainvillea_mazei_HV0266411
2KY819064-truncated-cdsKY819064-truncated.cds.fafafafaCDSChlorodesmis_fastigiata_HV0386511
3codonscodons.faCDScodonsfasta11
4fasta_alphabetfasta_alphabet.faCDSalphabetfasta1
5NC_026795-truncatedNC_026795-truncated.txtGenBankBryopsis_plumosa_WEST471811
6MH591083-truncatedMH591083-truncated.gbGenBankFlabellia_petiolata_HV0120211
7MH591084-truncatedMH591084-truncated.gbGenBankFlabellia_petiolata_HV0120211
8MH591085-truncatedMH591085-truncated.gbGenBankFlabellia_petiolata_HV0120211

Orthofinder

Alignment

Supermatrix

Gene Tree

OG0000002

OG0000005

Supertree

idx: 5 dist: 0.6931 support: 0.8700 height: 1.0000 name: 50.87idx: 6 dist: 0.6931 support: 0.8700 height: 1.0000 name: 60.87idx: 7 dist: 0.0000 support: 0.0000 height: 1.6931 name: 70.0Avrainvillea_mazei_HV02664Bryopsis_plumosa_WEST4718Flabellia_petiolata_HV01202Chlorodesmis_fastigiata_HV03865Caulerpa_cliftonii_HV03798

Workflow

Bibliography

File(s) not Fasta or Genbank file.

Suffix from file 'KY819064-truncated.cds.fafafafa' is not Fasta or Genbank. File is assumed to be in Fasta format.
Suffix from file 'NC_026795-truncated.txt' is not Fasta or Genbank. File is assumed to be in Fasta format.
Taxon/taxa is/are missing from phylogenetic tree.

The following taxon/taxa has/have no orthougroups with current configurations:
alphabetfasta
codonsfasta
Translation table value missing and unable to retrieve from file, default has been used.

Translation table for file fasta_alphabet.fa alphabetfasta is missing 
and could not be retrieved from text so default '1' has been used.
File(s) and/or sequence(s) not valid IGNORED
File 'invalid.gb' for taxon 'invalidgenbank' does not contain any sequences IGNORED

Sequence in file 'alphabet.gb' for taxon 'alphabetgenbank' is not valid: Invalid pattern found in 'KX808498.1'.
Character 'U' at position 2 found which is not in alphabet 'ATCGNatcgn-'. IGNORED

File 'invalid.fa' for taxon 'invalidfasta' does not contain any sequences IGNORED

Sequence 'emptysequence' in file 'codons.fa' for taxon 'codonsfasta' is not valid: Sequence length of 'emptysequence' (0) is less than the minimum 1. IGNORED

Sequence 'fakesequence' in file 'fasta_alphabet.fa' for taxon 'alphabetfasta' is not valid: Invalid pattern found in 'fakesequence'.
Character 'h' at position 2 found which is not in alphabet 'ATCGNatcgn-'. IGNORED